Genomic diversity of 2010 Haitian cholera outbreak strains - PubMed (original) (raw)

. 2012 Jul 17;109(29):E2010-7.

doi: 10.1073/pnas.1207359109. Epub 2012 Jun 18.

Seon Young Choi, Mark Eppinger, Philip W Clark, Arlene Chen, Munirul Alam, Bradd J Haley, Elisa Taviani, Erin Hine, Qi Su, Luke J Tallon, Joseph B Prosper, Keziah Furth, M M Hoq, Huai Li, Claire M Fraser-Liggett, Alejandro Cravioto, Anwar Huq, Jacques Ravel, Thomas A Cebula, Rita R Colwell

Affiliations

Genomic diversity of 2010 Haitian cholera outbreak strains

Nur A Hasan et al. Proc Natl Acad Sci U S A. 2012.

Abstract

The millions of deaths from cholera during the past 200 y, coupled with the morbidity and mortality of cholera in Haiti since October 2010, are grim reminders that Vibrio cholerae, the etiologic agent of cholera, remains a scourge. We report the isolation of both V. cholerae O1 and non-O1/O139 early in the Haiti cholera epidemic from samples collected from victims in 18 towns across eight Arrondissements of Haiti. The results showed two distinct populations of V. cholerae coexisted in Haiti early in the epidemic. As non-O1/O139 V. cholerae was the sole pathogen isolated from 21% of the clinical specimens, its role in this epidemic, either alone or in concert with V. cholerae O1, cannot be dismissed. A genomic approach was used to examine similarities and differences among the Haitian V. cholerae O1 and V. cholerae non-O1/O139 strains. A total of 47 V. cholerae O1 and 29 V. cholerae non-O1/O139 isolates from patients and the environment were sequenced. Comparative genome analyses of the 76 genomes and eight reference strains of V. cholerae isolated in concurrent epidemics outside Haiti and 27 V. cholerae genomes available in the public database demonstrated substantial diversity of V. cholerae and ongoing flux within its genome.

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Conflict of interest statement

The authors declare no conflict of interest.

Figures

Fig. 1.

Fig. 1.

Source and distribution of isolates collected during the 2010 Haitian cholera outbreak. Yellow and blue circles indicate sites where clinical and environmental strains were collected, respectively. Left: Distribution of strains with respect to different locations of sample collection in Haiti.

Fig. 2.

Fig. 2.

Neighbor-joining trees showing phylogenetic relationships based on 992 orthologous protein-coding genes (∼989,552 bp) of (A) 96 V. cholerae genomes representing diverse serogroups (strains with blue and green color represent Haitian environmental and clinical isolates, respectively), (B) V. cholerae non-O1/O139 strains representing clinical non-O1/O139 group 2, and (C) V. cholerae O1 and O139 strains representing the seventh pandemic cluster.

Fig. 3.

Fig. 3.

Polymorphisms in Haitian outbreak and reference isolates as determined by whole-genome mapping. Polymorphism detected in (A) TLC element, (B) MSHA gene clusters, (C) tRNA region, and (D) ICE element. Highlighted by the blue colored crossed line box are regions where polymorphisms were detected.

Fig. 4.

Fig. 4.

Whole-genome map similarity cluster of Haitian outbreak isolates with reference strains by using unweighted pair group method with arithmetic mean: (A) Chromosome I and II of each isolates clustered together; (B) similarity cluster of V. cholerae O1 based on chromosome I; and (C) similarity cluster of V. cholerae O1 based on chromosome II.

Fig. 5.

Fig. 5.

SNP-based phylogenetic tree for V. cholerae O1, constructed by using 277 intra- and intergenic SNPs identified in the V. cholerae O1 population, revealing clustering and radial expansion of the Haitian V. cholerae strains.

Fig. P1.

Fig. P1.

Neighbor-joining trees showing phylogenetic relationships based on 992 orthologous genes encoding proteins (∼989,552 nucleotide base pairs) of (A) 96 V. cholerae genomes representing diverse serogroups [strains indicated in blue and green represent Haitian environmental (HE) and clinical isolates (HC), respectively] and (B) V. cholerae O1 and O139 strains representing the seventh pandemic cluster. The seventh pandemic is the current and ongoing pandemic affecting almost every continent.

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